Abstract
BACKGROUND: Grain colour is an important quality trait affecting the market value and consumer preference. Chickpeas with black-coloured seed coat is known for their beneficial high antioxidant and fibber content, yet the underlying molecular basis remains poorly understood. RESULTS: Here, we examined the grain colour trait of a panel of 261 diverse desi chickpea (Cicer arietinum) accessions and specially characterized the development of the black seed coat. We showed that the black colouration emerged on embryo tips at 30 days after flowering (DAF) and expanded to whole grain at 35 DAF. Genome-wide association analyses revealed a single major genetic locus CaBlk3-1 on chromosome Ca3 controlling black seed coat. Candidate gene screening within 0.5 Mb upstream and downstream of CaBlk3-1 identified a single MYB-encoding gene CaMYB114 related to anthocyanin biosynthesis. Phylogeny analyses showed that CaMYB114 was clustered with Arabidopsis MYB90, MYB113, MYB114, consistent with their role in anthocyanin production. Subsequent qRT-PCR analyses suggested that CaMYB114 was abundantly transcribed in black genotypes but weakly in the brown genotypes at 35 DAF, closely linked with black colour development. Genetic variation analyses of CaMYB114 identified a 12-bp deletion containing a GAGA motif in the 5UTR region of black chickpea genotype. A gene-specific marker targeting this deletion was developed to validate its link with the black seed coat in a larger chickpea germplasm collection. CONCLUSIONS: We identified a single major QTL and the underlying candidate gene CaMYB114 closely associated with the black seed coat trait in chickpea. Our study has greatly improved our understanding of the genetic basis of chickpea black seed and will unlock the potential for breeding new chickpeas with desired grain colour to meet various market requirements. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-07544-0.